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Created September 17, 2021 11:00
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No output when streaming files from stding to bbtools [tadpole]: problematic case
cat o10to12_test_TTCACCGGTCTTGCTCCGTCCTGATAGC_temp.fastq | tadpole.sh in=stdin.fastq out=from_stdin.fa k=80 mode=correct overwrite=True bm1=1 bm2=1 t=1 -Xmx6g mincontig=auto mincountseed=1 rcomp=f
/gnu/store/60inp2szi6c7fbdq9nkgn7dz3pvlf8zl-openjdk-11.28-jdk/bin/java -ea -Xmx6g -Xms6g -cp /gnu/store/f7q0xsx6wkrag1skhkbammjqx9i28xkz-bbmap-38.90/share/java/BBTools.jar assemble.Tadpole in=stdin.fastq out=from_stdin.fa k=80 mode=correct overwrite=True bm1=1 bm2=1 t=1 -Xmx6g mincontig=auto mincountseed=1 rcomp=f
Executing assemble.Tadpole2 [in=stdin.fastq, out=from_stdin.fa, k=80, mode=correct, overwrite=True, bm1=1, bm2=1, t=1, -Xmx6g, mincontig=auto, mincountseed=1, rcomp=f]
Version 38.90
Using 1 threads.
Executing ukmer.KmerTableSetU [in=stdin.fastq, out=from_stdin.fa, k=80, mode=correct, overwrite=True, bm1=1, bm2=1, t=1, -Xmx6g, mincontig=auto, mincountseed=1, rcomp=f]
Set threads to 1
K was changed from 80 to 78
Initial:
Ways=31, initialSize=128000, prefilter=f, prealloc=f
Memory: max=6442m, total=6442m, free=6436m, used=6m
Initialization Time: 0.066 seconds.
Loading kmers.
Estimated kmer capacity: 131792503
After table allocation:
Memory: max=6442m, total=6442m, free=6321m, used=121m
After loading:
Memory: max=6442m, total=6442m, free=6316m, used=126m
Input: 119 reads 26894 bases.
Unique Kmers: 1277
Load Time: 0.120 seconds.
Reads Processed: 119 0.99k reads/sec
Bases Processed: 26894 0.22m bases/sec
Extending/error-correcting/discarding.
After extending reads:
Memory: max=6442m, total=6442m, free=6312m, used=130m
Input: 0 reads 0 bases.
Output: 0 reads 0 bases.
Errors detected: 0
Errors corrected: 0 (0 reassemble)
Reads with errors detected: 0 (NaN%)
Reads fully corrected: 0 (NaN% of detected)
Reads partly corrected: 0 (NaN% of detected)
Rollbacks: 0 (NaN% of detected)
Extend/error-correct time: 0.015 seconds.
Total Time: 0.225 seconds.
Reads Processed: 0 0.00k reads/sec
Bases Processed: 0 0.00m bases/sec
$ head from_stdin.fa
$
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